Yes. ClickGUARD's Google Ads tracking template works with parallel tracking. The only difference between using parallel tracking and the previous model is that ClickGUARD no longer forwards visitors to your landing pages as a proxy, but rather logs and processes information about the click in the background.
Are there any issues with custom tracking templates?
Even if you're using custom tracking templates on account (or lower) level ClickGUARD's tracking will not be affected by parallel tracking, as long as you used ClickGUARD's template merge tool.
Best approach is to remove lower-than-account level tracking templates and move the custom URL parameters into the final URL suffix setting.